# This file is the result of combining several RDB files, specifically # T0216.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0216.t2k.stride-ebghtl.rdb (weight 1.24869) # T0216.t2k.str2.rdb (weight 1.54758) # T0216.t2k.alpha.rdb (weight 0.659012) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0216.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0216 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0216.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 277 # # ============================================ # Comments from T0216.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0216 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0216.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 277 # # ============================================ # Comments from T0216.t2k.str2.rdb # ============================================ # TARGET T0216 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0216.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 277 # # ============================================ # Comments from T0216.t2k.alpha.rdb # ============================================ # TARGET T0216 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0216.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 277 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 K 0.0796 0.0169 0.9034 2 T 0.2273 0.0166 0.7561 3 I 0.1592 0.0186 0.8222 4 P 0.1237 0.0247 0.8516 5 S 0.1445 0.0711 0.7844 6 G 0.2133 0.0493 0.7374 7 K 0.4166 0.0308 0.5526 8 Y 0.6211 0.0104 0.3685 9 P 0.6287 0.0130 0.3583 10 V 0.8510 0.0077 0.1414 11 L 0.8433 0.0128 0.1439 12 M 0.6823 0.0177 0.3001 13 R 0.1896 0.0244 0.7860 14 N 0.0243 0.4632 0.5125 15 T 0.0138 0.7022 0.2840 16 A 0.0152 0.8207 0.1641 17 L 0.0081 0.9144 0.0774 18 L 0.0093 0.9166 0.0741 19 D 0.0078 0.9195 0.0727 20 L 0.0071 0.9245 0.0684 21 M 0.0081 0.9168 0.0751 22 E 0.0086 0.8704 0.1210 23 M 0.0119 0.8250 0.1630 24 F 0.0325 0.7429 0.2246 25 I 0.0335 0.6326 0.3339 26 P 0.0393 0.5777 0.3830 27 M 0.0323 0.6529 0.3149 28 I 0.0797 0.5558 0.3645 29 S 0.0838 0.4878 0.4284 30 A 0.0384 0.7370 0.2247 31 E 0.0358 0.7628 0.2015 32 N 0.0509 0.7771 0.1720 33 V 0.0552 0.7760 0.1689 34 Q 0.0667 0.6559 0.2774 35 K 0.0485 0.3758 0.5757 36 N 0.0537 0.1375 0.8088 37 L 0.0949 0.0908 0.8143 38 S 0.1373 0.1458 0.7168 39 P 0.0499 0.5718 0.3783 40 L 0.0378 0.6409 0.3212 41 K 0.0362 0.6928 0.2710 42 G 0.0416 0.5928 0.3655 43 K 0.0644 0.5135 0.4221 44 L 0.0760 0.2956 0.6283 45 G 0.0749 0.1026 0.8225 46 E 0.3254 0.0838 0.5909 47 Q 0.5959 0.0590 0.3451 48 V 0.5873 0.0642 0.3485 49 G 0.4485 0.0412 0.5103 50 N 0.2308 0.0607 0.7085 51 P 0.1506 0.1327 0.7167 52 A 0.3714 0.0740 0.5546 53 V 0.6395 0.0178 0.3426 54 S 0.7474 0.0129 0.2397 55 I 0.7213 0.0457 0.2330 56 K 0.5575 0.0904 0.3522 57 D 0.3625 0.0747 0.5628 58 L 0.1659 0.0372 0.7969 59 P 0.0612 0.1603 0.7785 60 Y 0.0878 0.1538 0.7584 61 H 0.1071 0.1318 0.7611 62 P 0.0448 0.1691 0.7861 63 K 0.0556 0.1121 0.8323 64 G 0.1265 0.0872 0.7863 65 L 0.2078 0.0976 0.6946 66 S 0.2311 0.0758 0.6932 67 S 0.2687 0.0606 0.6708 68 T 0.2966 0.0534 0.6500 69 P 0.3247 0.0551 0.6202 70 F 0.4108 0.0599 0.5292 71 D 0.2160 0.0645 0.7195 72 D 0.0684 0.1816 0.7500 73 E 0.0719 0.0736 0.8545 74 G 0.0794 0.0604 0.8602 75 V 0.1377 0.0364 0.8260 76 P 0.2810 0.0733 0.6457 77 T 0.2513 0.1028 0.6459 78 T 0.3303 0.1302 0.5394 79 E 0.3276 0.1468 0.5255 80 K 0.4666 0.1405 0.3929 81 F 0.5609 0.0938 0.3453 82 V 0.6255 0.1649 0.2096 83 L 0.5579 0.2128 0.2293 84 E 0.4363 0.2352 0.3285 85 N 0.2037 0.1109 0.6854 86 G 0.2622 0.0605 0.6773 87 V 0.6210 0.0634 0.3156 88 L 0.6760 0.1264 0.1976 89 K 0.5005 0.2593 0.2402 90 T 0.4543 0.2692 0.2766 91 F 0.3700 0.3032 0.3267 92 L 0.3654 0.2834 0.3512 93 H 0.2291 0.3122 0.4588 94 N 0.1139 0.2737 0.6124 95 L 0.0089 0.8832 0.1079 96 K 0.0065 0.9280 0.0655 97 T 0.0070 0.9420 0.0510 98 A 0.0066 0.9477 0.0457 99 R 0.0066 0.9350 0.0584 100 K 0.0069 0.9066 0.0865 101 E 0.0435 0.4780 0.4784 102 G 0.0398 0.0438 0.9164 103 V 0.0817 0.0210 0.8974 104 E 0.1497 0.0301 0.8203 105 P 0.1485 0.0807 0.7708 106 T 0.1428 0.0927 0.7645 107 G 0.1143 0.0990 0.7867 108 N 0.1386 0.1014 0.7601 109 G 0.1336 0.0817 0.7847 110 F 0.1142 0.0623 0.8234 111 V 0.1313 0.0453 0.8234 112 G 0.1853 0.0535 0.7612 113 G 0.2234 0.0551 0.7214 114 I 0.2547 0.0820 0.6633 115 R 0.3129 0.0695 0.6176 116 P 0.3450 0.0732 0.5818 117 V 0.4045 0.0699 0.5255 118 N 0.6204 0.0396 0.3400 119 L 0.7182 0.0204 0.2614 120 M 0.8052 0.0147 0.1802 121 L 0.7550 0.0160 0.2290 122 M 0.4812 0.0194 0.4995 123 P 0.1827 0.0542 0.7631 124 G 0.0557 0.0510 0.8933 125 E 0.1009 0.0330 0.8662 126 K 0.1350 0.0227 0.8423 127 S 0.1211 0.0154 0.8635 128 F 0.0057 0.9031 0.0913 129 E 0.0048 0.9315 0.0637 130 E 0.0050 0.9397 0.0553 131 L 0.0060 0.9419 0.0521 132 L 0.0076 0.9071 0.0853 133 K 0.0092 0.7309 0.2599 134 E 0.0212 0.6208 0.3579 135 M 0.0990 0.3356 0.5654 136 D 0.0599 0.1562 0.7839 137 R 0.1248 0.0946 0.7805 138 G 0.6460 0.0321 0.3219 139 V 0.8828 0.0091 0.1080 140 V 0.9080 0.0081 0.0839 141 I 0.8769 0.0089 0.1143 142 T 0.7347 0.0385 0.2268 143 E 0.5522 0.0345 0.4133 144 V 0.4237 0.0898 0.4865 145 E 0.3662 0.0817 0.5521 146 G 0.3210 0.0879 0.5911 147 M 0.3018 0.1120 0.5861 148 H 0.3433 0.1016 0.5551 149 A 0.3532 0.1040 0.5429 150 G 0.3904 0.0773 0.5323 151 A 0.4199 0.0522 0.5278 152 N 0.3317 0.0385 0.6299 153 S 0.1677 0.2163 0.6160 154 I 0.1334 0.2130 0.6535 155 S 0.2079 0.1541 0.6380 156 G 0.2920 0.0689 0.6391 157 E 0.5268 0.0473 0.4259 158 F 0.7676 0.0166 0.2158 159 S 0.7751 0.0179 0.2069 160 L 0.7754 0.0186 0.2060 161 F 0.7274 0.0227 0.2499 162 A 0.6517 0.0219 0.3264 163 K 0.6071 0.0346 0.3583 164 G 0.7438 0.0186 0.2375 165 Y 0.8498 0.0085 0.1417 166 W 0.8993 0.0062 0.0945 167 V 0.8578 0.0101 0.1321 168 E 0.6944 0.0535 0.2522 169 N 0.0932 0.0196 0.8872 170 G 0.0863 0.0302 0.8836 171 E 0.6921 0.0091 0.2988 172 I 0.8740 0.0040 0.1220 173 A 0.8117 0.0197 0.1686 174 H 0.7699 0.0121 0.2180 175 G 0.6953 0.0220 0.2826 176 V 0.6201 0.0224 0.3575 177 E 0.5489 0.0662 0.3849 178 D 0.5021 0.0628 0.4351 179 I 0.6002 0.0634 0.3363 180 T 0.7787 0.0443 0.1770 181 I 0.7827 0.0498 0.1675 182 S 0.5688 0.1015 0.3297 183 G 0.2880 0.1072 0.6047 184 N 0.1822 0.0876 0.7302 185 F 0.0109 0.8507 0.1384 186 L 0.0048 0.9461 0.0491 187 D 0.0048 0.9479 0.0473 188 L 0.0049 0.9462 0.0489 189 L 0.0053 0.9292 0.0655 190 R 0.0069 0.8687 0.1244 191 K 0.0114 0.7516 0.2369 192 I 0.0620 0.6367 0.3014 193 V 0.1457 0.5668 0.2876 194 L 0.2114 0.4988 0.2898 195 V 0.2505 0.3663 0.3832 196 G 0.1758 0.2357 0.5885 197 N 0.1058 0.2236 0.6706 198 D 0.1457 0.2621 0.5922 199 V 0.2169 0.3134 0.4698 200 K 0.3346 0.2433 0.4221 201 V 0.3560 0.1920 0.4520 202 S 0.2605 0.1019 0.6376 203 Q 0.1313 0.1230 0.7457 204 H 0.0911 0.0745 0.8344 205 T 0.2034 0.0635 0.7331 206 I 0.2475 0.0428 0.7096 207 A 0.1670 0.0344 0.7986 208 P 0.2330 0.0274 0.7396 209 S 0.6909 0.0202 0.2889 210 V 0.8809 0.0063 0.1128 211 L 0.9039 0.0049 0.0912 212 V 0.8356 0.0069 0.1575 213 E 0.5666 0.0534 0.3800 214 V 0.4103 0.0364 0.5533 215 L 0.7578 0.0094 0.2328 216 D 0.8781 0.0061 0.1158 217 V 0.8689 0.0099 0.1212 218 A 0.6200 0.0385 0.3415 219 G 0.3044 0.0259 0.6697 220 K 0.0511 0.0423 0.9066